Biowulf High Performance Computing at the NIH
Trimgalore on Biowulf

Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load trimgalore
[user@cn3144 ~]$ trim_galore inputfile

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. trimgalore.sh). For example:

#!/bin/bash
set -e
module load trimgalore
trim_galore inputfile [options...]

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] trimgalore.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. trimgalore.swarm). For example:

cd dir1; trim_galore infile
cd dir2; trim_galore infile
cd dir3; trim_galore infile
cd dir4; trim_galore infile

Submit this job using the swarm command.

swarm -f TEMPLATE.swarm [-g #] --module trimgalore
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module Loads the module for each subjob in the swarm